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High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI - Mol. Biol. Cell (2010)

Bottom Line: We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy.The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner.Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

ABSTRACT
The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

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Related in: MedlinePlus

Investigation of the relationship between nucleolar-genomic ratios and gene expression levels for each somatic chromosome. Nucleolar-genomic ratios plotted as a function of gene expression level for each somatic chromosome (expression data were not available for the X and Y chromosomes). Each point corresponds to the same 250-kbp bins as used in Figures 2B and 7 and Figure S2. The dashed line indicates the background level, normalized to a value of 1.0 (as described in Materials and Methods).
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Figure 8: Investigation of the relationship between nucleolar-genomic ratios and gene expression levels for each somatic chromosome. Nucleolar-genomic ratios plotted as a function of gene expression level for each somatic chromosome (expression data were not available for the X and Y chromosomes). Each point corresponds to the same 250-kbp bins as used in Figures 2B and 7 and Figure S2. The dashed line indicates the background level, normalized to a value of 1.0 (as described in Materials and Methods).

Mentions: The ratio of the nucleolar sequence read counts to those for genomic (nucleolar-genomic) was determined for each bin. The nucleolar-genomic ratios were then normalized to establish an appropriate background level. For this, chromosomal regions with no obvious nucleolar signal were selected as background and the nucleolar-genomic ratios were divided by the mean ratio in these regions. The background regions were found by selecting the bottom 10% of bins with lowest nucleolar-genomic ratio in each chromosome separately. This way, the nucleolar-genomic peaks in all chromosomes are presented with respect to the constant background level of 1, as marked with dashed lines in Figures 2B, 7, and 8. It should be noted that the results of the statistical analysis carried out below do not depend on the background level selection.


High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI - Mol. Biol. Cell (2010)

Investigation of the relationship between nucleolar-genomic ratios and gene expression levels for each somatic chromosome. Nucleolar-genomic ratios plotted as a function of gene expression level for each somatic chromosome (expression data were not available for the X and Y chromosomes). Each point corresponds to the same 250-kbp bins as used in Figures 2B and 7 and Figure S2. The dashed line indicates the background level, normalized to a value of 1.0 (as described in Materials and Methods).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2965689&req=5

Figure 8: Investigation of the relationship between nucleolar-genomic ratios and gene expression levels for each somatic chromosome. Nucleolar-genomic ratios plotted as a function of gene expression level for each somatic chromosome (expression data were not available for the X and Y chromosomes). Each point corresponds to the same 250-kbp bins as used in Figures 2B and 7 and Figure S2. The dashed line indicates the background level, normalized to a value of 1.0 (as described in Materials and Methods).
Mentions: The ratio of the nucleolar sequence read counts to those for genomic (nucleolar-genomic) was determined for each bin. The nucleolar-genomic ratios were then normalized to establish an appropriate background level. For this, chromosomal regions with no obvious nucleolar signal were selected as background and the nucleolar-genomic ratios were divided by the mean ratio in these regions. The background regions were found by selecting the bottom 10% of bins with lowest nucleolar-genomic ratio in each chromosome separately. This way, the nucleolar-genomic peaks in all chromosomes are presented with respect to the constant background level of 1, as marked with dashed lines in Figures 2B, 7, and 8. It should be noted that the results of the statistical analysis carried out below do not depend on the background level selection.

Bottom Line: We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy.The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner.Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

ABSTRACT
The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

Show MeSH
Related in: MedlinePlus